As shown in Figure 2, three regions of similarity between afaD and aafB, at the DNA level, are interspersed by two dissimilar regions. We devised a PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) test for daaD/afaD and aafB using primers complementary to regions conserved between the two targets, and digesting the 333/339 bp product with the restriction enzyme AluI. The digestion generates two fragments for aafB (233 and 106 bp) and five fragments for the more GC rich daaD gene (123, 106, 50, 36 and 18 bp). As shown in Figure 4, whilst the smallest daaD fragments are not visible, the two profiles are easily distinguished on a
2% agarose gel. Figure 4 PCR-RFLP to distinguish daaD and daaD2 from aafB. Lane 1: 1 Kb Ladder Plus (Invitrogen); Lanes check details 2-6: AluI restricted amplicons from EAEC Temozolomide ic50 strain 042 (aafB), DAEC strains 1 (daaC2), 2 and 3 (daaC) and non-pathogenic strain HS. Lane 7: pBR322 Msp1 marker (NEB). In the eFT508 solubility dmso course of our investigations, we identified a third restriction profile, initially
from strain DAEC1 (Figure 4). We sequenced the amplified region from this strain and determined that although the probe showed a 100% identity with daaD over most of its sequence, there was a 60 bp region with no significant homology. We refer to this allele as daaD2, and have deposited the sequence in GenBank (Accession Number EU010380). daaD2 lacks the two AluI sites closest to the 5′ end of daaD (Figure 2), which lie within the non-conserved region, but otherwise is very similar to daaD. Digestion of the PCR product from this allele yields 3 fragments of 104, 109 and 120 bp, which are irresolvable on a 2% gel but produce a profile easily distinguished from that of aafB and daaD (Figure 4). We found that daaD was more common than daaD2 in our collection. Additionally, there are four sequences from strains bearing identical or nearly identical (>99% identity) daaD2 alleles already deposited Cediranib (AZD2171) in GenBank , but as many as 20 sequences from an equivalent number of strains with classic daaD alleles.
This does suggest that daaD may be the more common allele, but the epidemiological significance of the variation, if any, in these alleles is unclear. Discussion and conclusion There have been brief mentions of daaC hybridization with EAEC in the literature. In some studies, the hybridization of the daaC probe to enteroaggregative E. coli has been taken to mean that the strains in question harbour a daa adhesin target as well as aggregative adherence genes . Other workers have proposed that the hybridization signal arises from cross-hybridization at a single locus [21, 25]. Although the former situation is a possibility, particularly as aggregative fimbrial genes are plasmid-borne, in this study we implicate the aafC gene, predicted to encode the usher for AAF/II fimbriae, as a cross-hybridizing locus.